Magnesium in PDB 5dgk: Sccmec Type IV Cch - Active Helicase

The structure of Sccmec Type IV Cch - Active Helicase, PDB code: 5dgk was solved by P.A.Rice, I.Mir-Sanchis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.18 / 2.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	110.140, 110.140, 302.755, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 26.1

The binding sites of Magnesium atom in the Sccmec Type IV Cch - Active Helicase (pdb code 5dgk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sccmec Type IV Cch - Active Helicase, PDB code: 5dgk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sccmec Type IV Cch - Active Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sccmec Type IV Cch - Active Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:33.6 occ:1.00 O1B A:ANP701 1.9 27.2 1.0 O1G A:ANP701 2.0 18.2 1.0 O A:HOH801 2.0 28.2 1.0 O A:HOH802 2.0 28.2 1.0 O A:HOH804 2.0 30.4 1.0 OG A:SER217 2.1 26.5 1.0 HB2 A:SER217 3.1 31.8 1.0 CB A:SER217 3.1 26.5 1.0 PG A:ANP701 3.2 16.7 1.0 PB A:ANP701 3.2 16.7 1.0 O1A A:ANP701 3.4 16.7 1.0 HNB1 A:ANP701 3.4 20.0 1.0 N3B A:ANP701 3.5 16.7 1.0 HG21 A:THR308 3.5 32.2 1.0 H A:SER217 3.5 29.9 1.0 HB3 A:SER217 3.7 31.8 1.0 O3G A:ANP701 3.9 23.5 1.0 HG22 A:THR308 4.0 32.2 1.0 OD1 A:ASP263 4.1 27.3 1.0 O2B A:ANP701 4.1 22.9 1.0 OD2 A:ASP263 4.1 29.0 1.0 CG2 A:THR308 4.2 26.8 1.0 N A:SER217 4.2 24.9 1.0 CA A:SER217 4.2 27.0 1.0 O3A A:ANP701 4.3 18.0 1.0 OE1 A:GLU264 4.4 39.6 1.0 HB2 A:LYS216 4.4 29.7 1.0 HG23 A:THR308 4.4 32.2 1.0 O2G A:ANP701 4.4 16.7 1.0 PA A:ANP701 4.4 16.7 1.0 CG A:ASP263 4.5 28.0 1.0 HA A:SER217 4.6 32.4 1.0 HE2 A:LYS216 4.7 34.1 1.0 HB2 A:GLU264 5.0 53.9 1.0

Magnesium binding site 2 out of 2 in the Sccmec Type IV Cch - Active Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sccmec Type IV Cch - Active Helicase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:39.5 occ:1.00 OG B:SER217 2.0 30.8 1.0 O1G B:ANP701 2.0 19.5 1.0 O B:HOH801 2.1 25.5 1.0 O B:HOH808 2.1 28.2 1.0 O B:HOH803 2.1 16.7 1.0 O1B B:ANP701 2.3 19.4 1.0 HB2 B:SER217 2.9 28.3 1.0 CB B:SER217 3.0 23.6 1.0 PG B:ANP701 3.3 16.7 1.0 HB3 B:SER217 3.4 28.3 1.0 O1A B:ANP701 3.5 16.7 1.0 PB B:ANP701 3.5 16.7 1.0 HNB1 B:ANP701 3.5 20.0 1.0 HG21 B:THR308 3.6 28.7 1.0 N3B B:ANP701 3.6 16.7 1.0 HH22 A:ARG326 3.7 42.9 1.0 H B:SER217 3.7 26.0 1.0 OD2 B:ASP263 3.8 39.6 1.0 OD1 B:ASP263 4.1 26.2 1.0 O3G B:ANP701 4.1 24.6 1.0 HH12 A:ARG326 4.2 41.5 1.0 HG22 B:THR308 4.2 28.7 1.0 OE1 B:GLU264 4.2 66.6 1.0 CA B:SER217 4.2 21.6 1.0 HH22 A:ARG395 4.3 37.9 1.0 N B:SER217 4.3 21.7 1.0 CG2 B:THR308 4.3 23.9 1.0 CG B:ASP263 4.3 29.6 1.0 O2B B:ANP701 4.4 16.7 1.0 O2G B:ANP701 4.5 16.7 1.0 O3A B:ANP701 4.5 19.8 1.0 NH2 A:ARG326 4.6 35.8 1.0 PA B:ANP701 4.6 16.7 1.0 HA B:SER217 4.6 25.9 1.0 HG23 B:THR308 4.7 28.7 1.0 HB2 B:GLU264 4.7 68.9 1.0 HB2 B:LYS216 4.7 26.5 1.0 OE2 A:GLU282 4.8 63.7 1.0 HE2 B:LYS216 5.0 30.2 1.0 NH2 A:ARG395 5.0 31.6 1.0 NH1 A:ARG326 5.0 34.6 1.0

I.Mir-Sanchis, C.A.Roman, A.Misiura, Y.Z.Pigli, S.Boyle-Vavra, P.A.Rice. Staphylococcal Sccmec Elements Encode An Active Mcm-Like Helicase and Thus May Be Replicative. Nat.Struct.Mol.Biol. V. 23 891 2016.
ISSN: ESSN 1545-9985
PubMed: 27571176
DOI: 10.1038/NSMB.3286